Add optional constraints to win.ia and samp.ia by chromosome

[zkamvar]

Currently, samp.ia and win.ia don't take into account chromosome. This is especially important for win.ia because the positions might be relative to chromosome, screwing up the windowing. The process should be:

1. detect if there is positional data
2. detect if there is chromosomal data
3. detect if the positions are relative to chromosome
4. reassign positions if 3 is true.

Here's some example code assuming x is a genlight object:

if (is.null(position(x))){
  position(x) <- seq(nLoc(x))
}
pos <- position(x)
if (!is.null(chromosome(x))){
  # Each chromosome has it's own position.
  # In this case, get large round number for each chromosome break.
  maxp <- 10^ceiling(log(max(pos), 10))
  if (length(unique(pmin(pos))) < nLoc(x)){
    pos <- split(pos, chromosome(x))
    for (p in seq(pos)){
      if (p != 1){
        pos[[p]] <- pos[[p]] + (maxp*(p - 1))
      }
    }
    pos <- unlist(pos, use.names = FALSE)
  }
}

This will set up the positions for windowing.

[zkamvar]

Since samp.ia() doesn't care about position, this issue might be a bit moot for it. Given that, I'm declaring this as done since Saturnalia, 2016.